Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F3 I0 R1
|
560 |
56.4 |
4650532 |
94.9% |
4413354 |
59.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,508,088 |
C→A |
23.5% |
G615V (GGC→GTC) |
ypdD ← |
fused predicted PTS enzymes Hpr component, enzyme I component, and enzyme IIA component |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,508,088 | 0 | C | A | 23.5%
| 139.3
/ 21.1
| 55 | G615V (GGC→GTC) | ypdD | fused predicted PTS enzymes Hpr component, enzyme I component, and enzyme IIA component |
| Reads supporting (aligned to +/- strand): ref base C (27/15); new base A (7/6); total (34/21) |
| Fisher's exact test for biased strand distribution p-value = 5.29e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GGCTACTCATACTCAGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTTGCTGCAACATGCG > W3110S.gb/2508023‑2508158
|
ggCTACTCATACTCAGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGt > 1:3500630/1‑71 (MQ=255)
catactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCg > 1:4498549/1‑70 (MQ=255)
catactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAGttacc > 1:3244432/1‑65 (MQ=255)
atactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCa > 1:2012922/1‑66 (MQ=255)
atactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCa > 1:2018249/1‑66 (MQ=255)
atactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCAcc > 1:2831667/1‑68 (MQ=255)
atactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGc < 1:417601/70‑1 (MQ=255)
aGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGcc > 1:4137061/1‑71 (MQ=255)
aGCTCATCAAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCaa > 1:781101/1‑66 (MQ=255)
tCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCaaa > 1:4503226/1‑64 (MQ=255)
cATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTAcc > 1:987755/1‑71 (MQ=255)
cATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAg > 1:4213323/1‑52 (MQ=255)
tCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAGTTCACCGCa < 1:4525653/59‑1 (MQ=255)
ccAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCaaa > 1:937576/1‑60 (MQ=255)
ccAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATg > 1:162272/1‑62 (MQ=255)
ccAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTAc > 1:4505914/1‑67 (MQ=255)
ccAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCAt > 1:1201818/1‑71 (MQ=255)
cAGGCCCAGCCCAAGCAGTAGCGGCATATAACGGCTTTCACCGACCAGTTCACCGCa < 1:3995013/57‑1 (MQ=255)
ccagcccaAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGcc > 1:3877366/1‑58 (MQ=255)
ccagcccaAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAGTTCACCGCaaa > 1:323351/1‑54 (MQ=255)
gcccaAGCAGTAGCGGCAGATAACGGCTTTCACCGcc < 1:1132791/37‑1 (MQ=255)
cccaAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCt < 1:2555127/71‑1 (MQ=255)
ccaAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTg < 1:3062116/71‑1 (MQ=255)
caAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAGTTCACCGCaaa > 1:3728082/1‑48 (MQ=255)
gCAGTAGCGGCAGATAACGGCTTTCACCGACCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCt < 1:2814217/66‑1 (MQ=255)
aGTAGCGGCAGATAACGGCTTTCACCGACCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATgcgc < 1:4523455/71‑1 (MQ=255)
gTAGCGGCAGATAAGGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCAGCTGATGCGCa < 1:3178810/71‑1 (MQ=255)
tAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAg > 1:841079/1‑71 (MQ=255)
cGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTAccc < 1:2852069/47‑1 (MQ=255)
cGGCAGATAACGGCTTTCACCGACCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTgg < 1:89602/71‑1 (MQ=255)
gCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGt > 1:3765581/1‑70 (MQ=255)
aTAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTa > 1:992983/1‑71 (MQ=255)
aTAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTa > 1:1464028/1‑71 (MQ=255)
tAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTAt < 1:2861335/71‑1 (MQ=255)
tAACGGCTTTCACCGACCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTAt > 1:2329399/1‑71 (MQ=255)
aaCGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCAtt > 1:1519614/1‑42 (MQ=255)
aaCGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATgcg > 1:598859/1‑57 (MQ=255)
aCGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCa > 1:1766849/1‑58 (MQ=255)
aCGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTAtt < 1:3730444/70‑1 (MQ=255)
aCGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTAtt < 1:748707/70‑1 (MQ=255)
aCGGCTTTCACCGACCAGTTCACCGCAAATGCCTTCCCATTTGCCCCGCt < 1:3313116/50‑1 (MQ=255)
cGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTtg < 1:2655117/71‑1 (MQ=255)
ggCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCa > 1:3988327/1‑56 (MQ=255)
ggCTTTCACCGACCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGAt > 1:2321157/1‑51 (MQ=255)
cTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGa > 1:3858910/1‑48 (MQ=255)
cTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGa > 1:3853674/1‑48 (MQ=255)
tttCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCt < 1:2007578/45‑1 (MQ=255)
ttCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTtgctgc > 1:623726/1‑70 (MQ=255)
tCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTAtt > 1:707730/1‑63 (MQ=255)
tCACCGACCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACt > 1:4168716/1‑60 (MQ=255)
cACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACt > 1:53677/1‑59 (MQ=255)
cACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTTGCTGCaa < 1:3191622/70‑1 (MQ=255)
cACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTTGCTGCaa < 1:3085012/70‑1 (MQ=255)
aCCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTAt < 1:507000/60‑1 (MQ=255)
aCCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTTGCTGCAAc < 1:2813402/70‑1 (MQ=255)
gCCCAGTTCACC‑CAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTTGCTGCAACATgcg < 1:2173346/71‑1 (MQ=255)
cccAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTTGCTGCAACATgcg < 1:3666101/71‑1 (MQ=255)
|
GGCTACTCATACTCAGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTTGCTGCAACATGCG > W3110S.gb/2508023‑2508158
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
